Bookmarks

Bioinformatics Linklist

Courses and lectures

Bioinformatics - Online Courses and Tutorials
EMBRACE Network of Excellence
EMBNet Quick Guides
EMBNet Courses
Sequence Analysis with distributed Resources
Tutorial Protein Structures (EXPASY) SwissModel
CMBI Courses for protein structure
2Can Support Portal - Bioinformatics educational resource
Bioconductor Workshops
CBS Bioinformatics Courses
The European School In Bioinformatics (Biosapiens)

Institutes Centers Networks

Bioinformatics Institutes Germany

WSI Wilhelm-Schickard-Institut für Informatik - Universitaet Tuebingen
WSI Huson - Algorithms in Bioinformatics
WSI Prof. Zell - Computer Architecture
WSI Kohlbacher - Div. for Simulation of Biological Systems
WSI Nieselt - Integrated Transcriptomics
ZBIT - Zentrum Bioinformatik Tuebingen
ZBIT Bioinformatics Teaching in Tuebingen
MPI Biological Cybernetics Tuebingen
MPI Dev Biol Tuebingen - Protein Evolution (Lupas)
Bioinformatik und Information Mining (Berthold) Konstanz
Studiengang Bioinformatik Muenchen
Bioinformatik Studiengang FU Berlin
institute for bioinformatics and systems biology / mips
Bioinformatics University Bielefeld
Bielefeld Bioinformatics Medical Informatics Department
Bielefeld Biomathematics and Theoretical Bioinformatics
Bielefeld Genome Informatics
IZIB Interdisziplinaeres Zentrum fuer Bioinformatik Leipzig
ZBI - Zentrum Bioinformatik - University Saarland
MPI Informatics Saarland
Jena Center for Bioinformatics - JCB
BCB - Berlin Centre for Genome Based Bioinformatics
MPI for Molecular Genetics Berlin - Vingron Computational Molecular Biology
Zuse Institute Berlin
ZBH Zentrum Bioinformatik University Hamburg
DKFZ - iBioS Intelligent Bioinformatics Systems
HUSAR Bioinformatics Lab - Biocomputing Services at DKFZ
TU Braunschweig - Department of Bioinformatics and Biochemistry
Plant Bioinformatics Portal Bioinformatics Center Gatersleben-Halle

Networks Germany

NGFN - Nationales Genomforschungsnetz
GABI - Genomanalyse im biologischen System Pflanze
HepatoSys - Network Systems Biology

Networks and Centers Europe

EBI European Bioinformatics Institute
BioSapiens Network - European Virtual Institute for Genome Annotation
The Sanger Centre UK
CBS - Center for Biological Sequence Analysis Technical University Denmark
SIB - Swiss Institute of Bioinformatics
Pôle Bio-Informatique Lyonnais
SEQUOIA - Bioinformatics Lille
Systems Biology Net Spain
Institute Nacional de bioinforática Spain
prbb Barcelona Biomedical Research Park

Networks and Centers International

NCBI US National Center for Biotechnology Information
Kyoto University Bioinformatics Center Japan
UBC Bioinformatics Centre UBiC Canada
Bioinformatics.Org - The Open-Access Institute
Weizmann Institute Bioinformatics and Biological Computing Israel
Baylor College of Medicine HGSC
San Diego Supercomputer Center Biological Projects CA USA
J. Craig Venter Institute (ex TIGR) MD USA
Whitehead Institute MIT MA USA
Broad Institute Center for Genome Research
Stanford Genomic Resources CA USA
The Genomics and Bioinformatics Group National Cancer Institute USA

Systems Biology Germany

Systems Biology in Germany
FORSYS - Research Units for Systems Biology
SysMo Systems Biology of Microorganisms
HepatoSys - Network Systems Biology
CSB - Center Systems Biology Stuttgart
ZBSA - Center for Systems Biology Freiburg
FRISYS Freiburg Initiative for Systems Biology
FDM - Freiburg Center for Data Analysis and Modeling
System Biology and Bioinformatics Wolkenhauer Univ. Rostock
BIOMS - Center for Modelling and Simulation in the Biosciences Heidelberg
Systems Biology at the IST and ISYS at University of Stuttgart
MPI Dynamik komplexer Systeme - Magdeburg System Biology
Magdeburg Centre for Systems Biology
BioQuant Heidelberg
ViroQuant Heidelberg
EML Research gGmbH Heidelberg
Theoretical Biophysics Humboldt University Berlin
Bork Group at EMBL - Comparative Systems Analysis

Systems Biology Europe

European Research Area for Systems Biology ERASysBio
SystemsX - The Swiss Initiative in Systems Biology
YSBN The Yeast Systems Biology Network
SYSBIO Systems Biology and Bioinformatics Finland
SCMBB Bruxelles
Centre for Integrative Systems Biology London
Manchester Centre for Integrative Systems Biology
Warwick Systems Biology Centre (CSB)
Systems Biology Ireland
Netherlands Institute for Systems Biology (niSB)
Systems Biology Net Spain

Systems Biology International

The International Society for Systems Biology
Systems Biology Portal www.systems-biology.org
US National Centers of System Biology
Systems Biology at UC San Diego
Department of Systems Biology Harvard Medical School Boston USA
Institute for Systems Biology Seattle - USA
Center for the Study of Biological Complexity Richmond USA
Ottawa Institute of Systems Biology
The Systems Biology Institute - Tokyo
Institute for Advanced Biosciences Keio University

Organizations Conferences

Bioinformatik.de
Bioinformatics.Org - The Open-Access Institute
EMBNet Bioinformatics Network
Gesellschaft fuer Informatik - Fachgruppe Bioinformatik
GBM Gesellschaft fuer Biochemie und Molekularbiologie
ISCB - International Society for Computational Biology
GCB 2011 German Conference on Bioinformatics - Weihenstephan
GCB 2010 German Conference on Bioinformatics - Braunschweig
Bioinformatics Open Source Conference BOSC 2011 Vienna
Bioinformatics Open Source Conference BOSC 2010 Boston
ISMB ECCB 2011 Vienna
7th International Workshop on Data Integration in the Life Sciences 2010
12th International Conference on Systems Biology ICSB 2011, Heidelberg, Germany
11th International Conference on Systems Biology ICSB 2010, Edinburgh, UK
HUO 2011 10th World Congress Geneva
HUPO 2010 9th World Congress Sydney
18. Arbeitstagung Mikromethoden der Proteinchemie München 2011
Synthetic Biology 5.0 Conference Stanford, CA, USA

Journals

Bioinformatics
BioMed Central Bioinformatics
AMB Algorithms for Molecular Biology
BioData Mining
Briefings in Bioinformatics
Human Genomics
In Silico Biology
Journal of Computational Biology
Journal of Medical Internet Research
Nucleic Acids Research
Omics: A Journal of Integrative Biology
PLoS Computational Biology
Nature Omics Gateway
Proteomics
Molecular and Cellular Proteomics
Journal of Proteome Research
Clinical Proteomics
Proteomics - Clinical Applications
Current Proteomics
Journal of Proteomics and Bioinformatics
Briefings in Functional Genomics and Proteomics
Proteome Science
Electrophoresis
BioMed Central - Systems Biology Gateway
BMC Systems Biology
Molecular Systems Biology
BioSystems
IET Systems Biology
IET Synthetic Biology

Bioinformatics server

EBI European Bioinformatics Institute
NCBI US National Center for Biotechnology Information
GenomeNet WWW server Japan
Expasy Proteomics Server
EMBNet - A Quick Guide to Expasy
Pôle Bio-Informatique Lyonnais
Weizmann Institute Bioinformatics and Biological Computing
Baylor College of Medicine HGSC
Bioinformatics Software Server Lille
San Diego Supercomputer Center Biological Projects
Bielefeld University Bioinformatics Server
HUSAR Bioinformatics Lab - Biocomputing Services at DKFZ
The Genomics and Bioinformatics Group NCI

Databases

Sequences

Entrez Browser NCBI
SRSWWW EMBL-EBI
DBGET/LinkDB Integrated Database Retrieval System
BCM Search Launcher
GeneCards Weizmann
Genome Matrix databases information integration
RefSeq Reference Sequence NCBI
Unigene NCBI
Uniprot Universal Protein Resource Swiss-Prot/TREMBL/PIR
EMBNet QuickGuide Swissprot Trembl Databases
PIR - Protein Information Resource
IPI - International Protein Index EBI
Human Gene and Protein Database (HGPD)
Protein Identifier Cross-Reference Service
NCBI UniVec and VecScreen Vector contamination search
Public SRS installations | Biowisdom

Genomes

Ensembl Genome Browser
Entrez-Genome NCBI
Integr8 Proteome Analysis at EBI
GOLD: Genomes On Line Database v 3.0
CBS Genome atlas database
MIPS: Munich Information Centre for Protein Sequences
J. Craig Venter Institute (ex TIGR) MD USA
The Sanger Centre
Whitehead Institute
Broad Institute Center for Genome Research
GeneCards Weizmann
HGP - Human genome project information
Human Genome Resources NCBI
Mouse Genome Resources NCBI
Rat Genome resources NCBI
Fugu Fish Genome Project
ZFIN - Zebrafish information network
Wormbase C. elegans
C.elegans Blast server (Sanger Centre)
FlyBase Drosophila
Yeast Genome Database MIPS
Schizosaccharomyces pombe genome (Sanger Centre)
Neurospora crassa Database (Broad)
Neurospora crassa Database (MIPS)
Fungal Genetics Stock Center
tair - The Arabidopsis Information Resource
GABI Primary Database ( GabiPD ) - Genomanalyse Pflanze
Plant genomes (MIPS)
Maize Genetics and Genomic Database
International Rice Genome Sequencing Project
Potato Genome Sequencing Consortium

Protein structures

RCSB Protein Data Bank
Entrez-Structure
Conserved Domains Database NCBI
Protein Databank in Europe (PDBe)
Structures by electron microscopy at MSD
SWISS-MODEL
EMBNet - A Quick Guide to Swiss-Model
SCOP: Structural Classification of Proteins
Superfamily HMM models SCOP
CATH database of structural domains
Gene3D Structural and Functional Annotation
The DALI database
NCBI VAST structural alignments
ModBase - Comparative protein structure models
BALL and BALLView Visualization and Modelling Tools

Motifs Profiles Domains

Interpro Domain and Profile Database
ExPASy - PROSITE
ExPASy - ScanProsite tool
SIB myHits motif scan
PRINTS protein fingerprints
SMART - Simple Modular Architecture Research Tool
Blocks WWW Server
Block Search
The Sanger Centre Pfam Server
The Sanger Centre HMM Pfam Searcher
TIGRFAMs protein families HMM
ProDom conserved protein domains
CDD Conserved domains database NCBI
DomCut prediction of linker regions between functional domains
PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System
PIR iProClass Protein Classification
Superfamily HMM models SCOP
Gene3D Structural and Functional Annotation
ModBase - Comparative protein structure models
Interproscan
WebLogo
WebLogo Server
Human Protein Reference Database
PhosphoMotif Finder
ELM Eukaryotic Linear Motif Functional Site Prediction
Phospho.ELM Database of phosphorylation sites
NetworKIN kinase substrate relationship prediction
DIALIGN - multiple sequence alignments to find conserved regulatory elements
The Gibbs Motif Sampler
MEME MAST motif discovery and search

Pathways

KEGG: Kyoto Encyclopedia of Genes and Genomes
ExPASy - Biochemical Pathways
NCI BioCarta - Pathways
PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System
Signaling Gateway - Cell Signaling Resource Nature
Reactome Project
BioCyc Database Collection
MetaCyc Encyclopedia of Metabolic Pathways
NCI Nature Pathway Interaction Database
IUPHAR receptor database
LGICD Ligand-gated ion-channel database
AraCyc - Pathway Database of Arabidopsis thaliana
Invitrogen Pathways
NetPath human signal transduction pathways
BBID-Biological Biochemical Image Database
Signal Transduction - Biochemweb.org virtual library
BioPAX - data exchange for biological pathway data
visANT - Visual Analysis Tool for Biological Networks and Pathways
MapMan - integrative view of microarray data and metabolic maps
GenMAPP Gene Map Annotator and Pathway Profiler
Biological Networks
Comparative Pathway Analyzer
PaLS Pathway and Literature Strainer (gene set annotation tool)
ProdoNet Prokaryotic gene list pathway annotator
GraphWeb: analysis of biological networks
Network Analysis Tools (NeAT)

Enzymes

Enzyme Database - BRENDA
IntEnz EBI Enzyme Database
Catalytic Site Atlas - CSA (EBI)
REBASE The Restriction Enzyme Database
Protein Kinase Resource
Kinase.com Global kinome analysis
NetworKIN kinase substrate relationship prediction

Software

EBI: The BioCatalogue
Open Source Initiative OSI
Open Bioinformatics Foundation
SourceForge.net Open Source Resource
Bioinformatics.Org - The Open-Access Institute
BioPerl
BioPython
BioJava
BioRuby
BioBike (LISP)

Literature

Pub Med Central
Advanced PubMed Search
PubMed/Medline NLM Mesh Browser
PubMed Single Citation Matcher
NCBI Journal database
List of Journals Indexed for Medline
Scopus
Web of Science
Google Scholar
CiteSeer (Computer and Information Sciences)
Scirus
Espacenet - Europe's network of patent databases
REDI Databases of Baden-Wuerttemberg
BIOSIS Previews
Medline
OVID - Journals
DOAJ - Directory of open access journals
PLoS Public Library of Science
HighWire Press - Stanford University free full papers
WorldSciNet Search Engine - World Scientific
JSTOR - The Scholarly Journal Archive
Electronic Journals Library
Subito - German libraries combined paper delivery service
Crossref Search - commercial publishers worldwide common paper service
Wiley Interscience
Springer Link
IngentaConnect

Literature and Data Mining

Compendia

Arrowsmith text mining tool compendium
Literature mining for the biologist - Review
Linking publication, gene and protein data - Review
Biomedical language processing - What is beyond PubMed - Review
Text-mining and information-retrieval services for molecular biology - Review
Text mining in Biology - Martin Krallinger
PDG Course Text mining in Biomedical Literature March 2006
BioCreAtIvE Text mining challenge
TREC Genomics Track data mining competition
BioNLP information portal
BLIMP Biomedical Literature Mining Publications

Information retrieval and clustering

EBIMed Medline information retrieval and extraction
GoPubMed - Ontology based literature search
HubMed pubmed rewired
MyNCBI PubMed updating and alerting
PubCrawler PubMed GenBank Update Service
eTBlast - related articles to any text
CoPub Mapper Gene Co-Publication Text Mining
PubMatrix
NCBI Esearch Entrez Utility

Information Extraction and Mining

The Arrowsmith Project
BioIE - Extracting informative sentences
Chilibot - Mining PubMed for relationships
Textpresso
PubGene
XplorMed: eXploring Medline abstracts
iProLink integrated Protein Literature INformation and Knowledge
RLIMS-P Rule-based LIterature Mining System for Protein Phosphorylation
iHOP - Information Hyperlinked over Proteins
String: functional protein association networks
BITOLA - Biomedical Discovery Support System
ONDEX - Data integration and visualisation

Text entity recognition tools

AliasServer Protein synonym search
ARGH Biomedical Acronym Database
Text2Knowledge - Acronym, Gene Name, Synonym, Interaction Database
ABNER: A Biomedical Named Entity Recognizer

Literature mining software

RefViz
QUOSA Information Manager
TRANSINSIGHT
InforSense
BioLT Literature Mining Tool (Biomax Informatics AG)
FTI Technology e-discovery
KNIME - Konstanz Information Miner
Ariadne Genomics MEDSCAN
BITOLA - Biomedical Discovery Support System
ONDEX - Data integration and visualisation
HyBrow hypothesis testing software
R Text Mining Package

Alignment and database searches

WWW BLAST Database Searches at NCBI
EMBNet QuickGuide BLAST
Fasta3 Database Searches at the EBI
Sequence similarity searches at the EBI
MPsrch at EBI
BCM Search Launcher: Multiple Sequence Alignments
PeCoP Psi-Blast to find persistently conserved positions
PVS: Protein Variability Server - conserved epitope discovery
Dotter dot-matrix sequence comparison program
ClustalX
Tcoffee DNA, RNA, Protein alignment tools
mreps DNA tandem repeat identifier
YASS genomic DNA local alignment similarity search tool
Standalone BLAST
BLAST standalone setup for Windows PC
STRAP Interactive Structure based Alignment Program
GeneDoc Homepage
Jalview - Java alignment editor
BioEdit Sequence Alignment Editor for Windows 95/98/NT/XP

Sequence tools

Galaxy bioinformatics framework
Unipro UGENE: Integrated Bioinformatics Tools
BCM Sequence Utilities
SeWeR - Sequence Analysis using Web Resources
Sequence Manipulation Suite 2
Sequence Extractor cloning toolbox
ReadSeq
Webcutter 2.0
Reverse Complement of Sequence
Primer 3
PrimerX - mutagenic primer design
pDraw32 Acaclone Plasmid drawing
Savvy Plasmid Maps
European Molecular Biology Open Software Suite EMBOSS
Genome assembly by phred and phrap
EMBNet Quick Guides to phred and phrap
Oligo Heat Map hybridization analysis
Integrated DNA Technologies Oligo SciTools

Protein tools

NPS: Network Protein Sequence Analysis
pI/Mw tool - Expasy
PeptideMass - Expasy
ProtParam tool - Expasy
ProtScale - Expasy
ISREC SAPS server

Phylogenetics

PHYLIP
Inst. Pasteur Pylip Online Server
Phylip Online Help
Phylip Tutorial (Jarno Tuimala)
EMBNet A Quick Guide to PHYLIP
Phylogeny.fr - robust phylogenetic analysis for the non-specialist
MEGA phylogeny software
MacClade Home Page
PAUP
FORESTER phylogenomics software libraries
TreeView
Rod Page Software
Hypertree large tree displaying tool
PANDIT Protein and Associated NucleotideDomains with Inferred Trees
PeCoP Psi-Blast to find persistently conserved positions
Ribosomal Database Project
Phylogeny Web Servers List
PHYLIP Phylogeny Programs
The Tree of Life Home Page
Tree of Life Links
NCBI Taxonomy Browser

Annotation

Gene Function Resources

Gene Ontology (GO) Consortium
QuickGO - GO Browser at EBI
AmiGO - GO Browser
Ontology Lookup Service (OLS)
GOA - Gene Ontology Annotation Project at EBI
GOStat - find statistically overrepresented GO terms
Gene Ontology Tools for Gene Expression Analysis
Sequence Ontology Project
Online Mendelian Inheritance in Man
GeneCards Weizmann
Genetic Association Database

Integrated annotation services

NIH - DAVID Annotation tools
eFamily Project - Grid integrating of protein database annotations
DAS - Distributed Annotation System
DAS registry server at Sanger - available DAS servers
SPICE - DAS Client
EnsEMBL Genome Browser DAS client
Dasty - DAS client

Gene prediction services

Glimmer Microbial Gene-Finding System
NCBI Glimmer3
GrailExp Grail Experimental Gene Discovery Suite
BCM Gene Feature Searches
CBS HMMgene server
CBS NetGene2 server
CBS NetPlantGene server
CBS Genome Atlas
GeneMark
WebGeneMark
Eukaryotic WebGeneMark
GENSCAN (C. Burge)
SplicePredictor
ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences
EBI Wise2 matches protein to genomic DNA
Lowe Lab tRNAscan-SE Search Server

Promotor prediction services

CBS NetStart 1.0 server Translation Start
CBS Promoter 2.0 server
WWW Promotor Scan Pol II
EPD Eukaryotic promotor database
TFM Explorer
TFM-Scan
TFSEARCH - Transcription Factor Search
TRANSFAC database at Biobase Biological Databases
ORegAnno: Open Regulatory Annotation
JASPAR Transcription factor database
JASPAR Transcription factor database paper
MotifMogul - Multiple Transcription Factor Binding Sites Algorithms
Regulatory Sequence Analysis Tools (RSAT)
DIALIGN - multiple sequence alignments to find conserved regulatory elements
The Gibbs Motif Sampler
MEME MAST motif discovery and search
DiRE identification of DIstant Regulatory Elements of co-regulated genes
ConTra - identification of conserved transcription factor binding sites

Structures

Transmembrane features

TMHMM Server 2.0
Phobius - combined TM and signal peptide prediction
ISREC TMpred Server
SOSUI Structure prediction of membrane proteins
HMMTOP Prediction of transmembrane helices and topology
TMAP multiple sequence alignment protein prediction
TopPred - Topology prediction of membrane helices
PRED-TMBB transmembrane beta barrel prediction

3D structures

RCSB PDB Protein Data Bank - PDB
NCBI Structure
Protein Databank in Europe (PDBe)
Conserved Domain Database NCBI
Structures by electron microscopy at MSD
NCBI VAST structural alignments
SWISS-MODEL
EMBNet - A Quick Guide to Swiss-Model
EMBL Dali protein structure comparison server
The DALI database Dali Fold Classification
CPHmodels - Homology modeling
ModBase - Comparative protein structure models
SCOP: Structural Classification of Proteins
Superfamily HMM models SCOP
CATH Protein Structure Classification Database
Gene3D Structural and Functional Annotation
Ressource Parisienne en Bioinformatique Structurale (RPBS)
Tutorial Protein Structures (EXPASY) SwissModel

3D software

Rosetta
foldit - The Protein folding game
PyMOL molecular visualization system
BALL and BALLView Visualization and Modelling Tools
UCSF Chimera
TarFisDock identifying drug targets by docking
CAVER protein analysis and visulaization - pockets and tunnels
DeepView Swiss-PdbViewer
GENO3D : Automatic Modeling of Protein Structure
PredictProtein
Cn3D Home Page
Jmol
Open Rasmol
RasTop - Rasmol Graphical Interface
Chime
Polyview 3D web server for animated images
Biodesigner Molecular Modeling and Visualization
VMD - Visual Molecular Dynamics
Accelrys Discovery Studio Visualizer (free version)

Model building

Coot
O (Alwyn Jones)
Accelrys Discovery Studio
ARP/wARP
HKL X-ray crystallography package
XDS diffraction data processing
Mosflm diffraction data processing
Phaser crystallographic software
SHARP/autoSHARP
SHELX
Phenix
RefMac
Solve/Resolve
USF Uppsala software factory
CCMS XtalView
CCP4 Molecular Graphics
CCP4 Software for Molecular X-ray crystallography
CCP4 Scala - scale together multiple observations of reflections
CCP4 Molrep - automated program for molecular replacement
CCP4 SOLOMON - density modification (phase improvement) by solvent flipping
CNSsolve Crystallography and NMR system
EMAN 3D single particle image reconstruction
SPIDER and WEB EM 3D single particle image reconstruction

Signal peptides and localization

SignalP server
Phobius - combined TM and signal peptide prediction
PSORT WWW Server
iPSORT N-terminal protein sorting signals

Glycosylation and lipid modifications

NetNGlyc Server
NetOGlyc server
ExPASy - ScanProsite tool
LipoP 1.0 server gram negative lipoprotein prediction

Secondary structures

BCM Structure Prediction Tools
PredictProtein
JPRED Secondary structure prediction
JUFO neuronal network prediction server
PSIPRED Protein Structure Prediction Server
PROF - Secondary Structure Prediction System
ISREC COILS Server
NPS: Consensus secondary structure prediction
NPS : coiled-coils prediction
NPS: MLRC
NPS: HNN
NPS: SOPMA
NPS: GOR4
DSSP Kabsch Sander PDB secondary structure assignment
BotDB DSSP analysis
DSSPCont Rostlab
DomCut prediction of linker regions between functional domains

RNA

Unafold RNA folding services
Integrated DNA Technologies Unafold server
Vienna RNA secondary structure servers
ncRNA tools for sequence/structure analyses of non-conding RNAs
SARSA Structural Alignment of RNA Using a Structural Alphabet
MAGNOLIA advanced RNA sequence and structural alignment

Small molecules

Human Metabolome Database
KEGG Drug Database
KEGG Ligand Database
ChEBI - Chemical Entities of Biological Interest
MSD Ligand Chemistry in PDB
NCBI PubChem Compound
NCBI PubChem Substance
NLM SIS Chemical Information
NCI-3D Search
ChemIDplus
CHEMINFO: Chemical Information Sources from Indiana University
FAF-Drugs: Free ADME/tox Filtering
OpenBabel format conversion tool for drugs
Java Molecular Editor at RPBS
JME Molecular Editor by Peter Ertl
SuperPred Drug Target Prediction Server

Functional genomics

Transcriptomics databases

Microarray Bioinformatics at EBI
Arrayexpress at the EBI
Expression Profiler at EBI
Documentation for Expression Profiler
Gene Expression Atlas - Large Scale Meta-Analysis of Public Microarray Data
GEO Gene Expression Omnibus at NCBI
NCBI Sequence Read Archive
MaRe Microarray Retriever
Stanford Microarray Database
Yale Microarray Database
JCV Institute Genomics
NIH ENCODE Project: ENCyclopedia Of DNA Elements
NGFN German National Functional Genomics Network
Genevestigator
GeneCAT - Gene Co-expression Analysis Toolbox
CATMA - A complete Arabidopsis Transcriptome MicroArray
The Arabidopsis Information Resource - TAIR
AFGN Arabidopsis Functional Genomics Network
Microarray Gene Expression Data Society
Stanford Functional Genomics Facility

Transcriptomics tools

NIH - Guide to Microarray Data analysis
Microarray Tools at NCI
HSLS: Microarray, SAGE and other gene expression data analysis tools
J-Express microarray analysis free version
MicroArray Explorer tool for Data Mining Gene Expression Patterns
Tools from the Eisen Lab
BioConductor Project - Open Source Software for Bioinformatics
R and Bioconductor Manual (Thomas Girke)
Babelomics - Systems biology microarray data mining
TIGR Microarray Software
RNA-Seq software ERANGE
Broad Institute Genecluster 2.0
dChip Software: Gene Expression Microarray and SNP Microarray Analysis
NASC Affymetrix Service: Analysis hints
Analysis of Affymetrix data using Excel
Affymetrix - NetAffx TM Analysis Center
MapMan - integrative view of microarray data and metabolic maps
GenMAPP Gene Map Annotator and Pathway Profiler

Proteomics databases and search engines

ExPASy Swiss 2Dpage
WORLD-2DPAGE Index to 2D-PAGE databases and services
ExPASy Peptide Mass Tool
ExPASy Mass Search
ExPASy MultIdent Peptide Mass Fingerprinting Tool
MASCOT Peptide Mass Fingerprint
SEQUEST MS proteomics search engine
Phenyx MS protein search engine (GeneBio/SIB)
X! Tandem MS search engine
OMSSA ms/ms search engine
UCSF Mass Spectrometry Facility Protein Prospector
PROWL protein and MS tools
PRIDE - Proteomics Identifications Database
PeptideAtlas
GPMDB proteomics database
Human Protein Atlas
Tranche - Secure P2P for Scientific Data Dissemination
ISPIDER MS meta protein database search
Protein Identifier Cross-Reference Service
NIH Histone Sequence Database
Phospho.ELM Database of phosphorylation sites
PhosphoPep Phosphopeptide systems biology database
Human Protein Reference Database

Proteomics post translational modifications

ExPASy - FindMod tool
ExPASy - QuickMod - MS/MS modified peptide search tool
RESID Database of protein modifications
Delta Mass PTM database (ABFR)
Unimod database - protein modifications for MS
Unimod - Modification naming guidelines
PRIDE Modification Search
PRIDE modification ontology lookup service (OLS)
ExPASy - Sulfinator tool Tyr sulfination sites predictor
NetPhos 2.0 Server STY phosphorylation site predictor
HUPO PSI Protein Modification Documentation

Proteomics software

TPP Trans-Proteomic Pipeline
SASHIMI MS proteomics pipeline
OpenMS / TOPP open source MS proteomics pipeline
MaxQuant
ICPLQuant
Scaffold protein identification framework (by Proteome Software)
mMass - Open Source Mass Spectrometry Tool
PeptideProphet MS proteomics prediction tool
ProteinProphet MS proteomics prediction tool
MassTRIX Metabolomics mass to pathway mapper

Proteomics organisations and standards

HUPO - Human Proteome Organisation
UniProt Chordata protein annotation program
HUPO Proteomics Standards Initiative
MASC Arabidopsis Proteomics Standards Subcommittee
mzML Specification | HUPO Proteomics Standards Initiative
Mass spectrometry data formats - Wikipedia
gabi Arabidopsis Proteomics Data
Proteomics from Angelika Görg
Boston University Biology Proteomics Resource
Deutsche Gesellschaft für Proteomforschung
Swiss Proteomics Society
SWISS Proteomics Society Proteomics Links
Proteome commons
ISB NHLBI Seattle Proteome Center
IonSource Proteomics Resource Links

Protein-Protein Interactions

EBI IntAct Project
DIP - Database of Interacting Proteins
DIP DLRP Database of Interactiong Proteins
BOND - Biomolecular Object Network Database
BioGRID - General Repository for Interaction Datasets
MINT - Molecular Interactions database
GNP Genome Network Platform
MIPS MPact Protein Interaction and Complex DB
MIPS Mammalian Protein-Protein Interaction Databank
The JCB Protein-Protein Interaction Website
GeneInfinity's Protein Interaction Analysis page
HPRD Human Protein Reference Database
Human Protein Interaction Database
NCBI HIV Human protein interaction database
UniHI MDC Unified Human Interactome
MIPS Yeast Protein-Protein-Interaction and Complex Viewer
Yeast Protein complex database
HomoMINT predicted human interaction network
PIPs Human Protein Interaction Prediction Database
Domino Domain peptide interaction database
VirusMINT
OPHID Interologous interaction database
PathBlast - Comparison of interaction networks between organisms
iHOP - Information Hyperlinked over Proteins
String: functional protein association networks
3DID - 3D interacting domains
DOMINE Database of Protein Domain Interactions
PSI-MI HUPO Standard for interactions
BioPAX - data exchange for biologicaql pathway data
Graphviz - Open Source Graph Visualization Software
Cytoscape - open source software for interaction visualization and integration
Osprey - protein interaction viewer
Osprey - protein interaction molecular modeling
visANT - Visual Analysis Tool for Biological Networks and Pathways
aiSee - commercial Graph layout software
NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto

miRNA

RNA Molecular Biology Tuschl Lab
miRBASE microRNA database Sanger Institute
Rfam RNA families database of alignments and CMs Sanger Institute
The siRNA user guide - Tuschl Lab
microRNA.org: A resource for predicted microRNA targets and expression
OligoWalk Web Server for siRNA design
AsiDesigner siRNA design pipeline

Systems Biology

System Biology Information Resources

BioModels.NET
The Reactome Project
Panther Classification Systems - Panther Pathways
Human Metabolome Database
KDBI - Kinetic Data of Biomolecular Interactions
SBML Systems Biology Markup Language
SBGN Systems Biology Graphical Notation Standardization
The International Society for Systems Biology
Systems Biology Portal www.systems-biology.org
The Systems Biology Institute - Tokyo
US National Centers for System Biology
Systems Biology at UC San Diego
Systems Biology in Germany
HepatoSys - Network Systems Biology
SystemsX - The Swiss Initiative in Systems Biology
YSBN The Yeast Systems Biology Network
Nature web focus: Systems biology: a user's guide
Systems Biology Wikipedia

Systems Biology Modeling Tools

Systems Biology WorkBench SBW package
JDesigner: A Biochemical Network Layout Tool
Jarnac biochemical simulation package
Pasadena Twain ODE solver of the SWB package
CADLIVE - network construction system
Dizzy stochastic simulations tool
CellDesigner - a modeling tool for biochemical networks
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
Cellware - Modeling and Simulation Tool
E-Cell project
COPASI - Complex Pathway Simulator
Gepasi - Biochemical Kinetics Simulator
Dynetica - a simulator of dynamic networks
JSim - a Java based simulation system
STOCKS - Stochastic kinetic simulations
Basis Gillespie Stochastic Simulator
CaliBayes - Bayesian calibration of biological simulators
JWS Online - Online Cellular Systems Modelling
PyBioS - web server for modeling and simulation of cellular systems
Virtual Cell Internet simulation server at NRCAM

Internet search

Search engines

Google
Bing
AltaVista
Yahoo!
Wolfram alpha
WebCrawler
MetaGer
CUSI - Suchmoeglichkeiten im Internet
W3 Search Engines FU Berlin

Link lists

Expasy
Expasy Life Science Directory
Bioinformatics Links Directory UBiC
HSLS: OBRC: Online Bioinformatics Resources Collection
Nucleic Acids Research Database Summary Paper List
Nucleic Acids Research Database Issue 2011
Nucleic Acids Research Database Issue 2010
Nucleic Acids Research Webserver Issue 2011
Nucleic Acids Research Webserver Issue 2010
CMS Molecular Biology Resource
Harvard Dept of MCB - Biology Links
CiteULike - online reference management sharing service
Connotea - online reference and link sharing
del.icio.us social bookmarking
Biotech Europe Link Base

Internet

Connected: An Internet Encyclopedia
RSS Tutorial for Content Publishers and Webmasters

Neural networks

SNNS Stuttgarter Neural Network Simulator
SNNS Download
Java-NNS University of Tuebingen
Java-NNS Download

Books

Bioinformatics (Mount) CSHL Press
Bioinformatics Baxevanis Ouellette Francis Wiley-VCH Ch. 5
Beginning Perl for Bioinformatics (Tisdall) O'Reilly
Mastering Perl for Bioinformatics (Tisdall) O'Reilly
Angewandte Bioinformatik (Selzer Marhoefer Rohwer) - Springer
Bioinformatik Interaktiv (Merkl, Waack) Wiley-Blackwell
Bioanalytik (Lottspeich Engels Joachim) Elsevier
Systems Biology: A Textbook (Wiley)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
Bioconductor Case Studies (Springer)
R Programming for Bioinformatics (CRC Press)
BLAST - (Korf, Yandell, Bedell) O'Reilly
Sequence Analysis in a Nutshell (Markel Leon) O'Reilly

The bioinformatics bench

Linux

Ubuntu Linux
Debian Linux
Open SUSE Linux
Professional SUSE Linux
Fedora Project
RedHat Linux
Linux Kernel Archives
BioLinux - Wikipedia
Knoppix
BioKnoppix
EMBNet A QuickGuide to UNIX
Linux Community (German)
linux.de

LAMP and WAMP

LAMP Wikipedia.de
LAMP Wikipedia.en
Comparison of WAMPs
XAMPP

Apache + HTML

Apache
SELFHTML

MySQL

MySQL
MySQL Community Server Download
MySQL Workbench Download
MySQL GUI Tools Download
MySQL reference manual

PHP

PHP
SELFPHP
phpMyAdmin
php-homepage.de - Resource fuer PHP und MySQL
PHP-Archiv - PHP Scripts

Perl

Perl
The Perl directory at perl.org
Perl documentation
Perl Download
ActiveState - ActivePerl Downloads
Strawberry Perl for Windows
CPAN PERL Script Archiv
Bioperl
Installing Bioperl on Windows - BioPerl
EMBNet QickGuides PERL and Regular Expressions

R and BioConductor

The R project for statistical computing
The Comprehensive R archive network
BioConductor Project - Open Source Software for Bioinformatics
R and Bioconductor Manual (Thomas Girke)
useR! 2011 R user conference Warwick, UK
useR! 2010 R user conference Gaithersburg, Maryland

Editors

The Vim Editor
Proton
Komodo

Laboratory tools

WETLAB: an open source electronic lab notebook
PHP Labware Project
OpenFreezer

EMBOSS

EMBOSS
EMBOSS wiki
EMBOSS application wiki
EMBOSS applications
EMBOSS applications program groups
EMBOSS for Windows
EMBOSS Users Guide
EMBOSS Developers Guide
EMBOSS Administrators Guide
EMBOSS user documentation
EMBOSS FAQ
EMBOSS Main Tutorial
EMBOSS mailing lists
EmbNet EMBOSS and wEMBOSS Quick Guides
JEMBOSS
wEMBOSS
Public SRS installations | Biowisdom

NCBI BLAST software

BLAST Wikipedia
BLAST setup procedure for Windows
NCBI BLAST download
BLAST FASTA databases download
BLAST standalone documentation

Open Source Bioinformatics Platforms

Galaxy bioinformatics framework
myGRID - Open Source Middleware Environment for Bioinformatics Workflows
TAVERNA Open Source Bioinformatics Workbench
eFamily Project - Grid integrating of protein database annotations
Bioclipse - visual platform for structural chemo- and bioinformatics
Systems Biology WorkBench SWB package
Mobyle web environment for bioinformatics workflows
Chinook P2P Bioinformatics Platform
Gaggle data management framework